Command line

Bandage can be run from the command line with this usage: Bandage <command> [options]

Type Bandage --help to see general help and Bandage <command> --help to see help for that particular command. The --helpall option will show all possible Bandage settings that can be specified on the command line.

Operating systems

Linux

Command line usage on Linux is straightforward. Either run Bandage from a particular directory (e.g. ./Bandage or ~/programs/Bandage) or copy it to a directory in your path to run it simply using Bandage.

Mac

Bandage for Mac is packaged as an application bundle which is actually a directory. To run Bandage via the command line, you must call the executable that is contained in the bundle: <path>/Bandage.app/Contents/MacOS/Bandage

Windows

Command line support is not fully functional on Windows. The program can be called with commands and options, and it should run correctly. But since Windows views it as a GUI application, not a command line application, there will be no output to the console.

No command

Usage: Bandage [options]

If Bandage is loaded from the command line without any particular command, it will simply launch the Bandage GUI. You can use command line options to adjust Bandage's settings.

Examples:

• Load Bandage with default settings:
  • Bandage
• Load Bandage and set edges to be wider and dark red:
  • Bandage --edgewidth 6.0 --edgecol darkred
• Load Bandage and turn on node name and node length labels:
  • Bandage --names --lengths

Bandage load

Usage: Bandage load <graph> [options]

When the load command is used, Bandage will load a graph immediately after opening. The --draw option will make Bandage draw the graph after loading it.

Examples:

• Load a graph but do not draw it:
  • Bandage load graph.fastg
• Load a graph and draw the entire graph:
  • Bandage load graph.fastg --draw
• Load a graph, conduct a BLAST search and draw the entire graph:
  • Bandage load graph.fastg --draw --query genes.fasta
• Load a graph, conduct a BLAST search and draw the region(s) of the graph surrounding BLAST hits:
  • Bandage load graph.fastg --draw --query genes.fasta --scope aroundblast --distance 3

Bandage image

Usage: Bandage image <graphfile> <outputfile> [options]

When the image command is used, Bandage will generate an image file without ever creating a GUI window.

Examples:

• Create a jpg image of the graph:
  • Bandage image graph.fastg image.jpg
• Create an svg image of the graph with uniform node colours:
  • Bandage image graph.fastg image.svg --colour uniform
• Create a png image of the region(s) of the graph surrounding BLAST hits:
  • Bandage image graph.fastg image.png --query genes.fasta --scope aroundblast --distance 3